Atomistry » Zinc » PDB 6i0w-6iiw » 6i84
Atomistry »
  Zinc »
    PDB 6i0w-6iiw »
      6i84 »

Zinc in PDB 6i84: Structure of Transcribing Rna Polymerase II-Nucleosome Complex

Enzymatic activity of Structure of Transcribing Rna Polymerase II-Nucleosome Complex

All present enzymatic activity of Structure of Transcribing Rna Polymerase II-Nucleosome Complex:
2.7.7.6;

Other elements in 6i84:

The structure of Structure of Transcribing Rna Polymerase II-Nucleosome Complex also contains other interesting chemical elements:

Magnesium (Mg) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Structure of Transcribing Rna Polymerase II-Nucleosome Complex (pdb code 6i84). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Structure of Transcribing Rna Polymerase II-Nucleosome Complex, PDB code: 6i84:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 6i84

Go back to Zinc Binding Sites List in 6i84
Zinc binding site 1 out of 8 in the Structure of Transcribing Rna Polymerase II-Nucleosome Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of Transcribing Rna Polymerase II-Nucleosome Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1801

b:0.7
occ:1.00
 SG A:CYS167 2.5 0.8 1.0
SG A:CYS110 2.5 74.3 1.0
SG A:CYS107 2.5 82.0 1.0
CB A:CYS107 3.0 82.0 1.0
SG A:CYS148 3.5 96.9 1.0
O A:GLY166 3.5 0.5 1.0
O A:CYS167 3.5 0.8 1.0
CB A:CYS110 3.7 74.3 1.0
CB A:CYS167 4.0 0.8 1.0
CB A:LYS112 4.3 80.6 1.0
C A:CYS167 4.3 0.8 1.0
CA A:CYS107 4.4 82.0 1.0
C A:GLY166 4.5 0.5 1.0
CB A:CYS148 4.5 96.9 1.0
O A:CYS107 4.5 82.0 1.0
C A:CYS107 4.6 82.0 1.0
CA A:CYS167 4.6 0.8 1.0
N A:CYS167 5.0 0.8 1.0
CA A:CYS110 5.0 74.3 1.0
N A:LYS112 5.0 80.6 1.0
O A:MET108 5.0 73.8 1.0

Zinc binding site 2 out of 8 in 6i84

Go back to Zinc Binding Sites List in 6i84
Zinc binding site 2 out of 8 in the Structure of Transcribing Rna Polymerase II-Nucleosome Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of Transcribing Rna Polymerase II-Nucleosome Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1802

b:67.0
occ:1.00
 SG A:CYS77 2.5 61.0 1.0
SG A:CYS67 2.5 79.2 1.0
CB A:CYS70 2.5 70.6 1.0
NE2 A:HIS80 2.6 63.3 1.0
SG A:CYS70 3.0 70.6 1.0
O A:CYS67 3.1 79.2 1.0
O A:CYS70 3.2 70.6 1.0
NE2 A:GLN68 3.2 81.0 1.0
CE1 A:HIS80 3.4 63.3 1.0
CB A:CYS67 3.5 79.2 1.0
CA A:CYS70 3.7 70.6 1.0
CD2 A:HIS80 3.7 63.3 1.0
C A:CYS70 3.8 70.6 1.0
O A:PRO78 4.0 56.0 1.0
CB A:CYS77 4.1 61.0 1.0
C A:CYS67 4.1 79.2 1.0
N A:CYS70 4.4 70.6 1.0
CA A:CYS67 4.4 79.2 1.0
CD A:GLN68 4.5 81.0 1.0
ND1 A:HIS80 4.6 63.3 1.0
CG A:HIS80 4.8 63.3 1.0
CA A:CYS77 5.0 61.0 1.0

Zinc binding site 3 out of 8 in 6i84

Go back to Zinc Binding Sites List in 6i84
Zinc binding site 3 out of 8 in the Structure of Transcribing Rna Polymerase II-Nucleosome Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of Transcribing Rna Polymerase II-Nucleosome Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1301

b:0.8
occ:1.00
 CB B:CYS1166 2.5 62.1 1.0
CB B:CYS1185 2.5 65.2 1.0
SG B:CYS1166 2.6 62.1 1.0
SG B:CYS1185 2.9 65.2 1.0
CA B:CYS1185 3.2 65.2 1.0
N B:CYS1166 3.4 62.1 1.0
CA B:CYS1166 3.5 62.1 1.0
O B:CYS1185 4.0 65.2 1.0
C B:CYS1185 4.1 65.2 1.0
N B:CYS1185 4.3 65.2 1.0
C B:ILE1165 4.5 68.9 1.0
CB B:ILE1165 4.5 68.9 1.0
CG2 B:ILE1165 4.6 68.9 1.0
C B:CYS1166 4.7 62.1 1.0

Zinc binding site 4 out of 8 in 6i84

Go back to Zinc Binding Sites List in 6i84
Zinc binding site 4 out of 8 in the Structure of Transcribing Rna Polymerase II-Nucleosome Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of Transcribing Rna Polymerase II-Nucleosome Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn401

b:0.6
occ:1.00
 N C:CYS92 2.2 90.0 1.0
SG C:CYS95 2.4 87.0 1.0
SG C:CYS88 2.4 0.6 1.0
CB C:CYS92 2.5 90.0 1.0
SG C:CYS92 2.5 90.0 1.0
C C:HIS91 2.7 0.8 1.0
CA C:CYS92 2.8 90.0 1.0
CA C:HIS91 3.1 0.8 1.0
SG C:CYS86 3.3 0.8 1.0
O C:HIS91 3.5 0.8 1.0
CB C:CYS88 3.6 0.6 1.0
CB C:CYS95 3.7 87.0 1.0
C C:CYS92 3.8 90.0 1.0
N C:HIS91 3.8 0.8 1.0
O C:CYS92 4.2 90.0 1.0
N C:CYS95 4.3 87.0 1.0
CB C:CYS86 4.4 0.8 1.0
CB C:HIS91 4.4 0.8 1.0
CA C:CYS95 4.5 87.0 1.0
N C:ASP93 4.6 80.5 1.0
C C:ASP90 4.7 0.1 1.0
CA C:CYS88 4.9 0.6 1.0
C C:CYS95 4.9 87.0 1.0
OG C:SER96 4.9 86.2 1.0
OG C:SER83 5.0 91.9 1.0
O C:ASP90 5.0 0.1 1.0

Zinc binding site 5 out of 8 in 6i84

Go back to Zinc Binding Sites List in 6i84
Zinc binding site 5 out of 8 in the Structure of Transcribing Rna Polymerase II-Nucleosome Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Structure of Transcribing Rna Polymerase II-Nucleosome Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn1201

b:0.4
occ:1.00
 SG I:CYS6 2.5 0.9 1.0
SG I:CYS31 2.5 0.1 1.0
CB I:CYS28 2.5 0.7 1.0
SG I:CYS28 2.5 0.7 1.0
SG I:CYS9 2.6 0.5 1.0
CB I:CYS6 3.1 0.9 1.0
CB I:CYS31 3.7 0.1 1.0
CA I:CYS28 4.0 0.7 1.0
N I:CYS31 4.0 0.1 1.0
CB I:CYS9 4.2 0.5 1.0
CA I:CYS31 4.3 0.1 1.0
CG I:ARG7 4.3 0.3 1.0
CB I:TYR33 4.3 92.5 1.0
C I:CYS31 4.4 0.1 1.0
N I:ARG7 4.4 0.3 1.0
N I:TYR33 4.5 92.5 1.0
CA I:CYS6 4.5 0.9 1.0
O I:CYS31 4.6 0.1 1.0
O I:ARG7 4.7 0.3 1.0
N I:CYS28 4.7 0.7 1.0
N I:ASN11 4.7 0.8 1.0
N I:ASN10 4.8 0.0 1.0
N I:ARG29 4.8 0.6 1.0
C I:CYS6 4.8 0.9 1.0
N I:SER32 4.8 99.8 1.0
C I:CYS28 4.8 0.7 1.0
NE I:ARG7 4.9 0.3 1.0

Zinc binding site 6 out of 8 in 6i84

Go back to Zinc Binding Sites List in 6i84
Zinc binding site 6 out of 8 in the Structure of Transcribing Rna Polymerase II-Nucleosome Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Structure of Transcribing Rna Polymerase II-Nucleosome Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn1202

b:0.0
occ:1.00
 SG I:CYS74 2.5 0.8 1.0
SG I:CYS77 2.5 0.6 1.0
N I:CYS77 2.5 0.6 1.0
CB I:HIS107 2.6 1.0 1.0
CB I:LYS76 2.7 0.8 1.0
CB I:CYS77 3.1 0.6 1.0
CG I:HIS107 3.3 1.0 1.0
C I:LYS76 3.3 0.8 1.0
CA I:LYS76 3.3 0.8 1.0
CA I:CYS77 3.4 0.6 1.0
N I:LYS76 3.6 0.8 1.0
CA I:HIS107 3.9 1.0 1.0
CG I:LYS76 3.9 0.8 1.0
CD2 I:HIS107 4.0 1.0 1.0
CB I:CYS74 4.0 0.8 1.0
N I:HIS107 4.1 1.0 1.0
CD I:LYS76 4.1 0.8 1.0
ND1 I:HIS107 4.1 1.0 1.0
C I:CYS77 4.3 0.6 1.0
O I:LYS76 4.5 0.8 1.0
N I:HIS78 4.5 0.7 1.0
O I:SER104 4.6 0.9 1.0
SG I:CYS105 4.6 0.5 1.0
CB I:CYS102 4.8 0.2 1.0
SG I:CYS102 4.8 0.2 1.0
C I:PRO75 4.9 0.3 1.0
NE2 I:HIS107 4.9 1.0 1.0
C I:HIS107 5.0 1.0 1.0
CE1 I:HIS107 5.0 1.0 1.0

Zinc binding site 7 out of 8 in 6i84

Go back to Zinc Binding Sites List in 6i84
Zinc binding site 7 out of 8 in the Structure of Transcribing Rna Polymerase II-Nucleosome Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Structure of Transcribing Rna Polymerase II-Nucleosome Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn101

b:42.9
occ:1.00
 O J:CYS7 2.1 45.5 1.0
SG J:CYS10 2.4 42.2 1.0
SG J:CYS7 2.4 45.5 1.0
CB J:CYS7 2.5 45.5 1.0
C J:CYS7 2.6 45.5 1.0
SG J:CYS46 3.0 34.0 1.0
CA J:CYS7 3.1 45.5 1.0
N J:CYS10 3.2 42.2 1.0
CB J:CYS10 3.4 42.2 1.0
N J:PHE8 3.6 42.6 1.0
N J:GLY11 3.6 40.1 1.0
CB J:CYS46 3.6 34.0 1.0
OG J:SER9 3.8 43.7 1.0
CA J:CYS10 3.8 42.2 1.0
N J:SER9 3.8 43.7 1.0
N J:CYS7 3.9 45.5 1.0
C J:CYS10 4.2 42.2 1.0
C J:SER9 4.2 43.7 1.0
CA J:CYS46 4.3 34.0 1.0
CA J:SER9 4.4 43.7 1.0
C J:PHE8 4.4 42.6 1.0
CB J:SER9 4.5 43.7 1.0
CA J:PHE8 4.6 42.6 1.0
O J:LYS12 4.6 38.8 1.0
NH2 J:ARG43 4.6 40.5 1.0
CA J:GLY11 4.6 40.1 1.0
N J:LYS12 4.7 38.8 1.0
C J:ARG6 4.8 39.7 1.0
O J:CYS45 4.8 32.9 1.0

Zinc binding site 8 out of 8 in 6i84

Go back to Zinc Binding Sites List in 6i84
Zinc binding site 8 out of 8 in the Structure of Transcribing Rna Polymerase II-Nucleosome Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Structure of Transcribing Rna Polymerase II-Nucleosome Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn101

b:0.1
occ:1.00
 OE1 L:GLU33 2.2 1.0 1.0
N L:GLU33 2.2 1.0 1.0
N L:CYS34 2.5 0.7 1.0
SG L:CYS31 2.5 0.8 1.0
CA L:GLU33 2.7 1.0 1.0
CB L:GLU33 2.7 1.0 1.0
C L:GLU33 3.0 1.0 1.0
SG L:CYS51 3.1 89.1 1.0
CD L:GLU33 3.1 1.0 1.0
C L:ALA32 3.2 0.8 1.0
N L:ALA32 3.4 0.8 1.0
CG L:GLU33 3.4 1.0 1.0
CB L:CYS31 3.5 0.8 1.0
CA L:CYS34 3.7 0.7 1.0
CA L:ALA32 3.8 0.8 1.0
C L:CYS31 3.9 0.8 1.0
O L:CYS34 4.0 0.7 1.0
SG L:CYS34 4.1 0.7 1.0
C L:CYS34 4.1 0.7 1.0
CB L:CYS34 4.1 0.7 1.0
O L:ALA32 4.2 0.8 1.0
O L:GLU33 4.2 1.0 1.0
OE2 L:GLU33 4.3 1.0 1.0
CB L:ALA32 4.3 0.8 1.0
CA L:CYS31 4.3 0.8 1.0
O L:CYS31 4.5 0.8 1.0
SG L:CYS48 4.5 95.2 1.0
CB L:CYS51 4.6 89.1 1.0

Reference:

L.Farnung, S.M.Vos, P.Cramer. Structure of Transcribing Rna Polymerase II-Nucleosome Complex. Nat Commun V. 9 5432 2018.
ISSN: ESSN 2041-1723
PubMed: 30575770
DOI: 10.1038/S41467-018-07870-Y
Page generated: Mon Oct 28 23:36:29 2024

Last articles

Mg in 6TRA
Mg in 6TR4
Mg in 6TR3
Mg in 6TMF
Mg in 6TQO
Mg in 6TQN
Mg in 6TQF
Mg in 6TQE
Mg in 6TQB
Mg in 6TQA
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy